sort BWA-MEM output directly avoiding intermediate write step

[sorelfitzgibbon]

I think the current steps:

bwa-mem2 \
      mem \
      -t ${task.cpus} \
      -M \
      ${alt_aware_option} \
      -R \"@RG\\tID:${header.read_group_identifier}.Seq${header.lane}\\tCN:${header.sequencing_center}\\tLB:${header.library_identifier}\\tPL:${header.platform_technology}\\tPU:${header.platform_unit}\\tSM:${header.sample}\" \
      ${ref_fasta} \
      ${read1_fastq} \
      ${read2_fastq} | \
samtools \
      view \
      -@ ${task.cpus} \
      -S \
      -b > \
      ${lane_level_bam}
   """
   }

followed by

samtools sort \
    -@ ${task.cpus} \
    -O bam \
    -o ${bam_output_filename} \
    ${sort_order} \
    ${input_bam}

could be replaced with a single process like this:

bwa-mem2 \
      mem \
      -t ${task.cpus} \
      -M \
      ${alt_aware_option} \
      -R \"@RG\\tID:${header.read_group_identifier}.Seq${header.lane}\\tCN:${header.sequencing_center}\\tLB:${header.library_identifier}\\tPL:${header.platform_technology}\\tPU:${header.platform_unit}\\tSM:${header.sample}\" \
      ${ref_fasta} \
      ${read1_fastq} \
      ${read2_fastq} | \
samtools sort \
     -@ ${task.cpus} \
     -o ${bam_output_filename} \
      -